9M3N | pdb_00009m3n

Crystal structure of human TRIM21 PRYSPRY in complex with T-02


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IWG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293The solution contained 0.1 M BIS-TRIS propane (pH 7.0) and 1.2 M potassium sodium tartrate tetrahydrate.
Crystal Properties
Matthews coefficientSolvent content
3.1160.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.04α = 90
b = 100.04β = 90
c = 50.7γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 6M2023-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.979183SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0835.6331000.017122.31.816022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.141000.20.9551.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.0835.6331598282699.9690.1940.19120.1890.23510.233846.893
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-3.993-3.9937.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.612
r_dihedral_angle_4_deg16.415
r_dihedral_angle_3_deg16.284
r_lrange_other8.885
r_lrange_it8.884
r_dihedral_angle_1_deg8.532
r_scangle_it6.734
r_scangle_other6.731
r_mcangle_it5.383
r_mcangle_other5.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.612
r_dihedral_angle_4_deg16.415
r_dihedral_angle_3_deg16.284
r_lrange_other8.885
r_lrange_it8.884
r_dihedral_angle_1_deg8.532
r_scangle_it6.734
r_scangle_other6.731
r_mcangle_it5.383
r_mcangle_other5.382
r_scbond_it4.461
r_scbond_other4.458
r_mcbond_it3.886
r_mcbond_other3.884
r_angle_refined_deg1.646
r_angle_other_deg1.252
r_symmetry_nbd_refined0.304
r_nbd_other0.264
r_symmetry_nbd_other0.188
r_nbd_refined0.187
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.145
r_symmetry_xyhbond_nbd_refined0.121
r_symmetry_nbtor_other0.082
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1440
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms31

Software

Software
Software NamePurpose
xia2data reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement